Super Autobacs, Up Garage, Yellow Hat, Autowave.
There is a huge difference between a mere "Autobacs" and a "Super Autobacs". The first is sort of like your corner Autozone, one rack of really expensive motor oils and one rack of air fresheners, and four walls and a roof. The second is a supermarket of goodies. Try to find the flagship or largest store in the city you are visiting, for the largest and most impressive displays. Minato Mirai and Nagoya Bay are big stores for Super Autobacs.
Up Garage is a used parts supermarket. Nakagawa Nagoya Store and Machida headquarters are good for Up Garage. But, if you are looking for something in particular, check their website or have the clerk go through their internet listings for the item, and they can transfer from store to store within their system.
Yellow hat is neat, but smaller, and Autowave ranks lower than Yellow Hat.

Takahara Book Store, Lindberg Book Store.
Some of the claim to fame of these is that they have the "biggest English language selection in Japan", which means they have or can get most of the stuff you can find on Amazon.Com. The more impressive stuff is in Japanese, and would never be found by an English speaking person. Both also have extensive sales brochure file cabinets, including some US market brochures, impossible to find, and sent to friends in Japan, who quickly hocked them for cash.

Don Quixote, Uniquelo.
Interesting discount and clothing stores. Uniuqulo prides itself on a line of automotive themed t-shirts, all in painfully small sizes for a westerner. Don Quixote is a discount department store ranging from censored adult DVDs and anime costumes to typical scale car models and evergreen tree air fresheners, and hits pots and pans and paper towels in between.

Every manufacturer has a museum and factory tour at their assembly plants. Mazda is Hiroshima, Nagoya is Toyota, Nissan has an engine museum in Yokohama, etc. Find where the build what you like, locate their plant, and find out how to get into their tour. All of these have historic displays too, not just current models.

Don't be surprised that tuner shops are little holes in the wall with one or two bays and no displays at all. At best, many make their bread and butter from ordinary repairs and do performance work on the side. The reason these places have international reputations is the knowledge in the
head of the owner/manager, and their ability to build fast cars, not their ability to have stacks of flashy stuff propped up in display cases (sort of changes your impression of some of the western tuning shops if you think about it).

Daikokufuto parking area on a Friday or Saturday night? Sorry, never been there on a weekend night, too many other things going on for the weekends for any personal information on this one. Umi Hotaru is a good parking area too.

Try the difference in quality at a Japanese McDonalds, where you will find actual crispy lettuce that does not try to crawl away from the burger while you eat it.
If you do not go to Moss Burger and have a Teriyaki Burger you should probably hide in shame and never admit you ever went to Japan at all.
If you have any appreciation of spicy food, stop by Little Spoon and Coco curry restaurants.
If you like egg and raw egg, most of the Japanese cuisine will be a breeze. If not, you are in for a long trip. The same for pork.

Some of the race tracks have amusement parks attached (like Suzuka). Actually, almost anything is an excuse for an amusement park or a shopping center.

There are more than a few very good go-cart tracks, all of which border on professional level compared to the West, and most of which have club membership members who go every day to hone their driving skills and really teach the tourists some humility.

Do yourself a favor and pick up an omamori at a shrine or temple, look for one for "driver safety". You will set yourself apart from the average ricer or superficial Japanophile and look like an expat or expert.

Take lots of business cards and little touristy type gifts from wherever you are from, to give to the people you meet. Learn and use introduction phrases, they will be impressed with your attempt and respond by going out of their way to help you. Learn the correct way to exchange business cards and feign interest in the writing on the business cards you receive.

Don't be surprised when the locals recoil away from you in terror, they've been blaming foreigners for all their problems for 2,000+ years.

When looking at a map and measuring how far apart things are, don't ever estimate travel time like you are in the US. 50 miles in the US might be under an hour on the highway in a car and a couple gallons of not too terribly overpriced gasoline. And parking is usually free. But in Japan, there are no straight roads and no straight line between two points. The highest speed limit on the most limited access highway is something like 40-50 MPH. Gasoline is two or three times more expensive. And anything larger than a foot path is a toll road that charges about a dollar or more per mile of pavement traveled. Going between two points takes a long time and a lot of money. And parking fees for garages and meters are obscene and there is no free parking.

Public transportation is good, but just about every possible route of travel involves 20+ minutes of walking to get to and from a train or subway station. Wear shoes that are comfortable to walk in and clothes that you can comfortably walk in at a brisk pace (just short of jogging) for a half hour or more at a time.
A rail pass pays for itself on the third decent length trip. You don't get to ride the fastest bullet train, or sit in the fancy seats, but getting there in an hour instead of 30 minutes still beats the alternative. There are several different rail companies, and not all participate in the rail pass program, so don;t be surprised if you do get to pay for some local subway and train trips, but always ask the ticket clerk.
There will be places not served by public transit. You probably won't find a rail stop close to a highway parking/service area, where car clubs and racers gather. Or near some mountain road or park. Or close to a little tuner shop out in the hinterland, surrounded by rice fields. Having a local friend with a car comes in handy. Taking a lot of gifts for that friend is a good idea, because they will be doing you significant favors and you will owe them a lot.

Addresses do not have street numbers with sequentially numbered locations. Postal addresses are based on mail delivery from a central location within each little postal carrier route. Finding a place is not as easy as looking at the street name and number and saying it's down the street from another known location. Websites, the backs of business cards, and advertisements, almost always have a map with significant land marks and roads to show locations of businesses. Be prepared to be lost. There is a reason that everyone in Japan has those strange antennas on their car, they are for the navigation systems. They don't go out without one.
If you do not have a hand held GPS device, this is your excuse to buy one. UDD has map files that can be loaded onto GPS units:
http://www.uud.info/They are not perfect. The maps are several years old (like there is no bridge shown between the mainland and Chubu/Centair Airport). You can't turn up the detail setting on your GPS all the way without blank spots in your map, because there is just too much stuff for the little GPS to handle. You can't type in an address and navigate like in the US. But you can mark a known point, locate a point by matching the image on the screen with the little printed map from a website or advertisement, or load in way points from a computer program. In the very least, you can walk around an area, without someone supervising you, and not worry about getting lost.

Kuro Neko/Black Cat is handy for moving suitcases and boxed items from place to place (hotel to hotel or house to house) when they are too big to carry on the train or haul. When looking to ship stuff back, check the post office first, they are the least expensive, but have size limits. Spoilers and grilles are too long. Wheels without tires are usually not too big, even boxed in a stack of four. They still have M-Bag Surface, and it's a lot less than air mail. Learn the size and weight limits, and shop accordingly. And remember that over stuffing a suitcase over the weight limit for the return trip can result in $500+ in additional luggage weight fees, and a burning in the stomach for not sticking more stuff into the mail for a fraction of that fee.

Further to the above about travel, visiting rural areas many Japanese will take the train to get there, and then hire a car for the day to get about, which works fairly well. Hire cars will probably have GPS too ! Some bits of highway are 100kmh (62mph), although it's true that a fair few are 80 or less. Tolls are not as much as a dollar per mile unless they've gone up a LOT lately !

Further to the above about travel, visiting rural areas many Japanese will take the train to get there, and then hire a car for the day to get about, which works fairly well. Hire cars will probably have GPS too ! Some bits of highway are 100kmh (62mph), although it's true that a fair few are 80 or less. Tolls are not as much as a dollar per mile unless they've gone up a LOT lately !

In an effort to promote tourism the law was changed in April so that you can now pay $10 to get on the highway until you get off. Only on weekends and holidays though.